BatchJobs v1.8
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Batch Computing with R
Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Functions in BatchJobs
Name | Description | |
batchExpandGrid | Map function over all combinations. | |
cfReadBrewTemplate | Cluster functions helper: Read in your brew template file. | |
callFunctionOnSSHWorkers | Call an arbitrary function on specified SSH workers. | |
makeClusterFunctionsSSH | Create an SSH cluster to execute jobs. | |
getResources | Function to get job resources in job function. | |
makeRegistry | Construct a registry object. | |
makeJob | Creates a job description. | |
getSSHWorkersInfo | Print and return R installation and other information for SSH workers. | |
showLog | Display the contents of a log file. | |
makeClusterFunctionsTorque | Create cluster functions for torque-based systems. | |
cfBrewTemplate | Cluster functions helper: Brew your template into a job description file. | |
debugMulticore | Helper function to debug multicore mode. | |
showStatus | Retrieve or show status information about jobs. | |
addRegistrySourceDirs | Add source dirs to registry. | |
cfHandleUnknownSubmitError | Cluster functions helper: Handle an unknown error during job submission. | |
sweepRegistry | Sweep obsolete files from the file system. | |
filterResults | Find all results where a specific condition is true. | |
batchQuery | Manually query the BatchJobs database | |
batchReduce | Reduces via a binary function over a list adding jobs to a registry. | |
addRegistrySourceFiles | Add source files to registry. | |
findJobs | Finds ids of jobs that match a query. | |
debugSSH | Helper function to debug SSH mode. | |
cfKillBatchJob | Cluster functions helper: Kill a batch job via OS command | |
batchUnexport | Unload exported R objects. | |
findDone | Find jobs depending on computional state. | |
getErrorMessages | Get error messages of jobs. | |
checkIds | Check job ids. | |
configuration | BatchJobs configuration. | |
getConfig | Returns a list of BatchJobs configuration settings | |
syncRegistry | Syncronize staged queries into the registry. | |
getJobLocation | Get the physical location of job files on the hard disk. | |
copyRequiredJobFiles | ONLY FOR INTERNAL USAGE. | |
getJobIds | Get ids of jobs in registry. | |
getJobParamDf | Retrieve Job Parameters. | |
getJobNr | Get number of jobs in registry. | |
getJobInfo | Get computational information of jobs. | |
makeClusterFunctionsSLURM | Create cluster functions for SLURM-based systems. | |
makeClusterFunctionsSGE | Create cluster functions for Sun Grid Engine systems. | |
reduceResults | Reduce results from result directory. | |
getJobResources | Function to get the resources that were submitted for some jobs. | |
removeRegistry | Remove a registry object. | |
loadExports | Load exported R data objects. | |
sanitizePath | Sanitize a path | |
killJobs | Kill some jobs on the batch system. | |
loadConfig | Load a specific configuration file. | |
getJobs | Get jobs from registry by id. | |
getLogFiles | Get log file paths for jobs. | |
dbGetJobs | ONLY FOR INTERNAL USAGE. | |
dbCreateJobDefTable | ONLY FOR INTERNAL USAGE. | |
loadRegistry | Load a previously saved registry. | |
removeRegistrySourceFiles | Remove source files from registry. | |
loadResult | Loads a specific result file. | |
setRegistryPackages | Set packages for a registry. | |
resetJobs | Reset computational state of jobs. | |
showClusterStatus | Show information about available computational resources on cluster. | |
makeClusterFunctionsLSF | Create cluster functions for LSF systems. | |
testJob | Tests a job by running it with Rscript in a new process. | |
loadResults | Loads result files for id vector. | |
makeClusterFunctions | Create a ClusterFuntions object. | |
setConfig | Set and overwrite configuration settings | |
makeClusterFunctionsLocal | Create cluster functions for sequential execution on local host. | |
setJobFunction | Sets the job function for already existing jobs. | |
updateRegistry | ONLY FOR INTERNAL USAGE. | |
waitForJobs | Wait for termination of jobs on the batch system. | |
setJobNames | Set job names. | |
getJob | Get job from registry by id. | |
makeClusterFunctionsInteractive | Create cluster functions for sequential execution in same session. | |
grepLogs | Grep log files for a pattern. | |
installPackagesOnSSHWorkers | Install packages on SSH workers. | |
removeRegistryPackages | Remove packages from registry. | |
makeClusterFunctionsMulticore | Use multiple cores on local Linux machine to spawn parallel jobs. | |
removeRegistrySourceDirs | Remove packages from registry. | |
makeClusterFunctionsOpenLava | Create cluster functions for OpenLava systems. | |
makeSSHWorker | Create SSH worker for SSH cluster functions. | |
makeSubmitJobResult | Create a SubmitJobResult object. | |
submitJobs | Submit jobs or chunks of jobs to batch system via cluster function. | |
sourceRegistryFiles | Source registry files | |
batchMapResults | Maps a function over the results of a registry by using batchMap. | |
batchExport | Export R object to be available on the slaves. | |
BatchJobs | The BatchJobs package | |
batchMap | Maps a function over lists or vectors, adding jobs to a registry. | |
batchMapQuick | Combination of makeRegistry, batchMap and submitJobs. | |
addRegistryPackages | Add packages to registry. | |
applyJobFunction | applyJobFunction ONLY FOR INTERNAL USAGE. | |
batchReduceResults | Reduces results via a binary function and adds jobs for this to a registry. | |
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Details
URL | https://github.com/tudo-r/BatchJobs |
BugReports | https://github.com/tudo-r/BatchJobs/issues |
MailingList | batchjobs@googlegroups.com |
License | BSD_2_clause + file LICENSE |
LazyData | yes |
ByteCompile | yes |
RoxygenNote | 6.1.1 |
Encoding | UTF-8 |
NeedsCompilation | no |
Packaged | 2019-05-09 08:41:04 UTC; lang |
Repository | CRAN |
Date/Publication | 2019-05-14 22:00:16 UTC |
imports | backports (>= 1.1.1) , brew , checkmate (>= 1.8.0) , data.table (>= 1.9.6) , DBI , digest , parallel , RSQLite (>= 1.0.9011) , sendmailR , stats , stringi (>= 0.4-1) , utils |
depends | BBmisc (>= 1.9) , methods , R (>= 3.0.0) |
suggests | MASS , testthat |
Contributors | Michel Lang, Bernd Bischl, Henrik Bengtsson |
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